In silico mutagenesis and docking studies of Pseudomonas aeruginosa PA-IIL lectin predicting binding modes and energies.
This article is focused on the application of two types of docking software, AutoDock and DOCK. It is aimed at studying the interactions of a calcium-dependent bacterial lectin PA-IIL (from Pseudomonas aeruginosa) and its in silico mutants with saccharide ligands. The effect of different partial charges assigned to the calcium ions was tested and evaluated in terms of the best agreement with the crystal structure. The results of DOCK were further optimized by molecular dynamics and rescored using AMBER. For both software, the agreement of the docked structures and the provided binding energies were evaluated in terms of prediction accuracy. This was carried out by comparing the computed results to the crystal structures and experimentally determined binding energies, respectively. The performance of both docking software applied on a studied problem was evaluated as well. The molecular docking methods proved efficient in identifying the correct binding modes in terms of geometry and partially also in predicting the preference changes caused by mutation. Obtaining a reasonable in silico method for the prediction of lectin-saccharide interactions may be possible in the future.
Adam
Jan
J
National Centre for Biomolecular Research, Department of Biochemistry, and Department of Chemistry, Faculty of Science, Kotlarska 2, Masaryk University, 611 37 Brno, Czech Republic.
Kríz
Zdenĕk
Z
Prokop
Mrtin Prokop
MP
Wimmerová
Michaela
M
Koca
Jaroslav
J
D018829:Adhesins, Bacterial / Q000737:chemistry* / Q000235:genetics*; D000595:Amino Acid Sequence; D001665:Binding Sites / Q000235:genetics; D002118:Calcium / Q000737:chemistry; D003198:Computer Simulation; D048088:Informatics; D037102:Lectins / Q000737:chemistry* / Q000235:genetics*; D008024:Ligands; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009005:Monosaccharides / Q000737:chemistry; D016297:Mutagenesis, Site-Directed / Q000706:statistics & numerical data*; D020836:Protein Structure, Quaternary; D011550:Pseudomonas aeruginosa / Q000737:chemistry* / Q000235:genetics*; D017386:Sequence Homology, Amino Acid; D012984:Software; D013816:Thermodynamics
D018829:Adhesins, Bacterial; D037102:Lectins; D008024:Ligands; D009005:Monosaccharides; C038692:adhesin, Pseudomonas; D002118:Calcium